Nucleotide polymorphism |
|
Number of segregating sites (S, s) |
Nei (9) |
Minimum number of mutations (H, η) |
Tajima (10) |
Nucleotide diversity (π) (with and without Jukes and Cantor correction) |
Nei (9); Jukes and Cantor (11) |
Theta (θ) per DNA sequence from S |
Tajima (12) |
Theta (θ) per site from S |
Nei (9) |
Theta (θ) per site from Eta (η) |
Tajima (10) |
Theta (θ) per site from π, from S and from η under the Finite Sites Model |
Tajima (10) |
Average number of nucleotide differences (k) |
Tajima (13) |
Tajima statistic test (D) |
Tajima (14) |
Total number of synonymous and non-synonymous sites |
Nei and Gojobori (15) |
Number of non-synonymous substitutions per non-synonymous site (Ka) and number of synonymous substitutions per synonymous site (Ks) |
Nei and Gojobori (15) |
Codon bias |
|
Relative Synonymous Codon Usage (RSCU) |
Sharp (16) |
Effective Number of Codons (ENC) |
Wright (17) |
Codon Adaptation Index (CAI) |
Sharp and Li (18) |
Scaled Chi Square |
Shields (19) |
G + C content in second, third and total positions |
Wright (17) |
Linkage disequilibrium |
|
Nucleotide distance (Dist) between a pair of polymorphic sites |
|
D |
Lewontin and Kojima (20) |
D′ |
Lewontin (21) |
R and R2
|
Hill and Robertson (22) |
ZnS statistic |
Kelly (23) |
Chi-square test |
|
Fisher's exact test |
|